Adding Letters to DNA’s Alphabet: Triumph or Travesty?

A group of synthetic biologists at the Scripps Research Institute recently announced that they have successfully expanded the genetic code of E. coli, inviting both praise and doubt from the scientific community.

The genome of an organism encodes the entirety of the set of proteins available for cells to express. The manner and the degree with which various genes are expressed give rise to the complexity and diversity of the flora and fauna we observe. The genome is composed of two pairs of nucleic acids (Adenine-Thymine and Guanine-Cytosine), and it is the order of these bases that provide the template for protein expression in a cell.

Earlier this May, the group published a paper in Nature that describes the research they conducted in support of their findings. According to the group, the two new bases are efficiently PCR amplified and transcribed in vitro, which means that bacterial machinery can accurately replicate a plasmid (a circular piece of DNA) containing the two new bases.

The group admits that with an expanded genetic alphabet, however, new challenges arise: 1) the unnatural base pairs (UBPs) must be present in the cell, 2) bacterial polymerases must be able to replicate the UBPs faithfully, and 3) the UBPs must be able to withstand the various proteins responsible for maintaining the integrity of DNA. However, the group addresses all three concerns through their research.

To tackle the first challenge, they attempted to allow the nucleotides to simply diffuse into the bacterial cytosol, but to no avail. They were able to achieve more success by transforming the bacteria with algal plastids. Then to allow replication of the UBPs by polymerase, they engineered the plasmid to focus replication of the UBPs by DNA polymerase I, instead of DNA polymerase III, which is the enzyme that normally replicates the majority of the genome. In addition, the group showed that even after a 15-hour period of growth, the UBPs remained and were not targeted by DNA repair pathways, indicating the UBPs’ ability to withstand mechanisms that normally correct DNA.

Although quite dense, the article introduces the “first organism that stably harbors DNA containing three base pairs.” The research brings up some of the potential promise found in the field of synthetic biology – most notably, that with an extended genetic alphabet, cells would be able to stitch together a much larger array of proteins, which could greatly expand the array of drugs available to treat disease. Furthermore, according to a NY Times article on the Nature article, the “work also gives some support to the concept that life can exist elsewhere in the universe using genetics different from those on Earth.”

This raises concern for some scientists, who say that humans are playing God, and more relevantly, that it is a safety issue. However, the authors maintain that these bacteria cannot replicate the UBPs outside of culture, as they need to be constantly provided the synthetic nucleotides. As for the theological concern some have, that is a question that is bound to resurface as the field of synthetic biology pushes forward in the next few decades.

However, there are many challenges facing the authors, the most troubling being that in order for the cells to replicate the incorporated UBPs, they must continually be fed free nucleotides. Another equally monumental challenge is that in order for this research to have the implications the authors suggest, a mechanism to introduce the new array of amino acids would need to be created. This is no easy task – even in the drawing boards: to begin with, scientists would somehow have to find a way to newly synthesize more tRNA sythetases (the enzymes that charge amino acids onto the corresponding tRNA molecules) with the same level of specificity as those generated by millions of years of evolution. In spite of these and other challenges, the authors present a thought-provoking discovery that will hopefully burgeon in the coming years.